The code adds some completely useless invisible (or rather white) stuff. The lines
\clip(0pt,403pt) -- (389.957pt,403pt) -- (389.957pt,99.6166pt) -- (0pt,99.6166pt) -- (0pt,403pt);
\color[rgb]{1,1,1}
\fill(3.76406pt,399.236pt) -- (380.923pt,399.236pt) -- (380.923pt,253.19pt) -- (3.76406pt,253.19pt) -- (3.76406pt,399.236pt);
\fill(53.4497pt,394.719pt) -- (374.901pt,394.719pt) -- (374.901pt,289.325pt) -- (53.4497pt,289.325pt) -- (53.4497pt,394.719pt);
draw a white background that is larger than the actual picture. TikZ sees that and thinks it is part of the picture. Simply removing/uncommenting these lines removes most of the whitespace.
Near the end of the first scope,
\color[rgb]{1,1,1}
\fill(3.76406pt,249.426pt) -- (386.193pt,249.426pt) -- (386.193pt,103.381pt) -- (3.76406pt,103.381pt) -- (3.76406pt,249.426pt);
does the same.
Additionally (near the end of the second scope
),
\pgftext[center, base, at={\pgfpoint{220.95pt}{106.392pt}}]{\sffamily\fontsize{9}{0}\selectfont{\textbf{ }}}
adds a blank node below the picture, again enlarging the bounding box.
Removing all those lines gives a tight bounding box.
As far as I know, TikZ cannot do the cropping for you, as it can't know whether the white stuff is intentional or not (there might for example be a dark background behind the image so that white is visible).
\documentclass[tikz,margin=10pt]{standalone}
\usepackage{mathtools,amssymb}
\begin{document}
\begin{tikzpicture}[scale=2,transform shape]
\draw (1,0) arc (0:90:1);
\draw (-1,0) arc (180:270:1);
\draw[fill=gray!30] (-1,0) -- (-2,0) arc (180:90:2) -- (0,1) arc (90:180:1);
\draw[fill=gray!30] (1,0) -- (2,0) arc (0:-90:2) -- (0,-1) arc (-90:0:1);
\node at (0.2,0.75) {\tiny $\phi^2$};
\node[rotate=50] at (-0.7,0.5) {\tiny $t=0$};
\node[rotate=50] at (0.7,-0.5) {\tiny $t=0$};
\node[rotate=50] at (-1.45,1.2) {\tiny $t=1$};
\node[rotate=50] at (1.45,-1.2) {\tiny $t=1$};
\node[rotate=50] at (-1.6,1.4) {\tiny $\partial \varphi (1)$};
\node[rotate=50] at (1.6,-1.4) {\tiny $\partial \varphi (1)$};
\node at (-2,2) {\tiny $\Omega_1$};
\node at (2,-2) {\tiny $\Omega_2$};
\node at (-1,1) {\tiny $\Delta \mathfrak{M}^2$};
\node at (1,-1) {\tiny $\Delta \mathfrak{M}^2$};
\end{tikzpicture}
\end{document}
Best Answer
And a version in Metapost, relying on the fact that the tangent point on the small circle must be the same
point
on the circumcircle, and using some nice colours.